Soran University
Faculty of Science
Department of Chemistry
2nd Stage
Unit Course book
Biochemistry
Unit Coordinator
Dr. Araz Muhammad Yousif
2014-2015
Contact hours a week: 2 hours theoretical; 3 hours practical
Total Credit: 3 units
Introduction:
Biochemistry is the branch of life science which deals with the study of chemical
reactions occurring in living cells and organisms. Life is a chemical process involving
thousands of different reactions occurring in an organized manner. These are called
metabolic reactions. Biochemistry is the study of the chemistry of biomolecules and living
organisms.
Objective:
The major objective of biochemistry is the complete understanding of all the
chemical processes associated with living cells at the molecular level and also to
diagnosis,and monitoring diseases. To achieve this objective, biochemists have attempted
to isolate numerous molecules found in cells, to determine their structures, concentrations
and to analyze how they function.
Course description:
To understand the main concept of human Biochemistry. Structures and chemical
properties of carbohydrates. lipids, protein, amino acids; and nucleic acid. protein
purification and characterization; protein structure and thermodynamics of polypeptide
chain folding; catalytic mechanisms, kinetics and regulation of enzymes; energetics of
biochemical reactions; metabolism; roles of coenzymes and prosthetic groups in redox
reactions; pathways for carbohydrate lipids , protein, amino acids ;and nucleic acid
metabolism, carbohydrate oxidation; glycogen metabolism; glucose synthesis; electron
transport and oxidative phosphorylation. Provide the student with the fundamental
understanding of life - Understand important issues in medicine, health, and nutrition.
Fundamental understanding, chemical structures, and reactivities of molecules that
participate in cellular reactions, biological function of cellular molecules,
Learning Outcomes:
By the end of the course students should be able to:
1. Appreciate why the broad spectrum of biochemistry is important in medicine,
agriculture, pharmaceuticals, and ethics;
2 Understand the: The principle of biochemistry by studying the biochemistry of
carbohydrate , protein ,hormones, enzymes & lipids
3. Understand the basis for the molecular structure of different biochemical compounds;
4 Understand the biosynthesis of basic biochemical “building blocks”;
5. Understand the conformation, dynamics, and function of proteins;
6. Understand the generation and storage of metabolic energy;
7- Understand overall aspects of the integration of metabolic processes; the role of
enzymes in metabolic function. The role of membranes in cell metabolism
8-The process of DNA replication, transcription and translation of genetic information and
DNA repair
The practical works
Identification of biomolecules. Study purification, extraction, or kinetics of the
biomolecules. Estimation of biomolecules e.g. glucose, cholesterol, TG, protein, and etc…
Provides students with a working knowledge of the macromolecules and
fundamental metabolic pathway
The practical works aim:
Provide the student with the fundamental understanding of life - Understand
important issues in medicine, health and nutrations. Includes all the tests that which can be
used for the diagnosis, monitoring, or treatment of the diseases.
Practical skills
Have developed the skills to accumulate, integrate, and apply biochemical
information in their own field e.g. hospitals, research center etc…..
Staff associated with the unit:
Staff
Room Number
Dr. Araz M. Yousif
Chemistry Dep. Room
Soran University- Faculty of Science
Department of Chemistry
Unit: Biochemistry
Email
araz_zangana@yahoo.com
Method of Assessment:
1 x 2 h lectures and 1 x 3 h laboratory sessions per week.
Examination and grading
Midterm:

Two Midterm exams for theoretical: 2 x 10%

Homework, reports, unknown, and Quizzes: 5%

One Practical exam: 15%

Total Mark: 40%

Final Exam:

One final written exam for theoretical: 40%

One final Written/practical for practical exam: 20%

Total Mark: 60%
Marking System
The grades for each piece of assessed work are as follows:






90-100 % is excellent
80-89% is very good
70-79% is good
60-69% is a moderate pass
50-59% is a pass
<49% is a fail
Unit Timetable/Content
University
Academic
Week
Lecture Title & Content
The Cell Structure and Function
1
Biochemistry of carbohydrate
Definition. Biomedical importance
Isomerism & their types. Chemistry of Carbohydrate.
Classification. Monosaccharides&their chemical reaction
,Trioses,Tetroses, Pentoses, and Hexoses
Pyranose &Furanose structures .Mutarotation
Formation of O- Glycosidic linkage & N—glycosidic linkage
.Disaccharides
Physical Properties. Structure
Reducing properties. Sucrose &its synthesis. Maltose &its
synthesis
- Lactose & its synthesis
2
-
3
-
4
5
6
Polysaccharides .Homopolysaccharides
Hetropolysaccharides. Glycogen
Starch (amylose &amylopectin)
Dextran. Cellulose.Carbohydrate Derivatives. Amino Sugar
Glycosugar. Mucopolysaccharides
a- Proteoglycan. Hepatin
b- Chondriotin Sulphate
c- Keratin Sulphate
d- Dermatin Sulphate
Biochemistry of Lipids
1-Classification of lipids –
A-Simple lipids
B- Complex lipids
-. Phospholipids -. Glycolipids:C-Derived lipids: 2-. Structure of lipids
.3-. Lipid function 4-. Triacylglycerols and fatty acids
5-. Membrane components and function
.6-. Cholesterol ..7-. Steroid hormones
Biochemistry of Proteins & Amino acids
Protein structure as the basis for protein function.
1. The specificity of protein structure
2. Biological Functions of protein
3. : Classification of protein
A. Simple protein: B. Conjugated Proteins
Nucleoprotein .Lipoprotein
Phosphoprotein .Metalloprotein
1. Glycoprotein. Fibrous proteins
. 3. Globular proteins. 4-Membrane proteins
Glycoproteins. 5-level of organization
A-Primary Structure of Proteins
B- Secondary Structure. C- Tertiary Structure. D- Quaternary
Structure
5-Denaturation of Proteins.
7
8
9
6-Peptides.7-. The peptide bond and its characteristics.8-Peptides
of Physiological Significance.Glutathione
9-. Amino acids.10-Stereochemistry
11-Classification of Amino Acids
12-Acid Base Properties of Amino Acids
13-Optically activity
Enzymes
1-General Properties 2-Nature of Enzymes
3-Classification of Enzymes
Class I. Oxidoreducatases
Class II. Transferases
Class III. Hydrolases
Class IV. Lyases:
Class V. Isomerases
Class VI. Ligases or synthetases.
4-Factors Affecting Enzyme Activity
.
1. Temperature
2. pH.3. Substrate/enzyme concentration etc.
5-Mechanism action of Enzymes 6-Enzyme Inhibition.
7- Regulation of Enzyme activity
8-Enzymes in clinical diagnosis.
9-Enzyme Kinetics
Lineweaver-Burk plot, significance of Vmax.and KM values, regulation of
enzyme action in cells, regulatory enzymes and their control, specificity
of enzymes.
10
10-Enzymes in clinical diagnosis.
Molecular Genetics
1-Structure of Nucleic acids .2-Types of Nucleic acids
3-Replication of DNA
4-DNA Damage and repair mechanism
5-RNA synthesis Post transcriptional Modifications
11
12
6-Translation/Protein synthesis. .7- Regulation of protein synthesis
8-The Genetic code
Vitamins and Coenzymes
1-Water soluble vitamins
2-Chemistry, sources, function and deficiency of:
Thamine .Riboflavin ..
Niacin. Pyridoxine . Biotin . Cobalamin
Folic acid . Panthothenic acid . Ascorbic acid
Deficiency, symptoms and side effects in over dosage
2-Fat soluble vitamins
13
14
15
Chemistry, Sources, function, deficiency and Hypervitaminosis of:
Vitamin A
Vitamin D.
Vitamin E. Vitamin K.
Deficiency, symptoms and side effects in over dosage
Hormones
1-Definition and classification
2-Biosynthesis, storage, transport .
3-Mechanism of action of steroid hormones
4-Mechanism of action of protein hormones
5-Receptors and diseases
6-Second messengers.
7-Insulin synthesis, secretion and metabolic role
8-Diabetes mellitus
Symptoms and complications of DM.
9-Glucagon .Clinical aspects
10-Thyroxin .Synthesis and Metabolism
-Hypothyroidism and Hyperthyroidism
Goiter . Catecholamines
Overview of metabolism: catabolism and anabolism
16
Integrative Metabolism Bioenergetics
1-Introduction
2- Structural basis of high energy phosphate
3-Formation and utilization of ATP
4-Catabolism of fuel molecules
5-Concept of Free energy .
6-Oxidation-reduction reactions
7-Aerobic energy generation
17
18
8-Electron transport system and oxidative Phosphorylation .
9-Respiratory control.
Carbohydrate Metabolism
1-Digestion and absorption of Carbohydrates.
2-Glycolysis
.Glycolysis: first phase
Glycolysis: second phase
2-Kreb’s cycle. -Function and regulation of kreb’s cycle.
3-Glycogen Metabolism
19
20
21
23
4- Glycogen storage diseases.
5- Pentose phosphate pathway
6- The Cori - cycle.
7-Gluconeogenesis
Lipid Metabolism.
1-Digestion and absorption of Lipids
2-Metabolism of Fatty acids and Triacyl Glycerols .
3-β-Oxidation of Fatty acids
4-Metabolism of Ketone bodies
5-Biosynthesis of Fatty acids and triacyl glycerols
6-Cholesterol Metabolism.
-Atherosclerosis. 8-Hypercholesterolemic drugs
9-Lipid storage diseases. 10-Fatty Liver..
11-Lipoproteins .12-Chemical compositions of Membranes
13- Metabolism of phospholipids
Protein metabolism
1-Digestion and absorption of proteins
2-Amino acid catabolism
3-Nitrogen balance, excretion
4- The urea cycle in organisms
5-Protein metabolism and nitrogen .
6- Biosynthesis of Amino Acids,
7- disorders in protein metabolism.
Nucleic acids metabolism
-Digestion and absorption of Nucleic acids
-DNA and RNA catabolism
Nucleic acids catabolism
Biosynthesis of Nucleic acids
Biosynthesis of DNA and RNA
- disorders in Nucleic acids metabolism.
Practicals Associated with this Unit:
University Academic
Week
1
Experiment
Carbohydrates
Qualitative tests for Carbohydrates
1- Molisch,s test
2- Benedict’s test:
2
Qualitative tests for Carbohydrates(continue)
3- Barfoed’s test:
4- Selivanoffe’s test:
5- Bail's test:
3
Music acid test
Ketoses test test for sucrose
Acid hydrolysis of disaccharide
4
Scheme for the identification of an unknown carbohydrate
It is examination about the carbohydrates by using the scheme
6- Scheme for the identification of an unknown carbohydrate…
5
Carbohydrate and polarity phenomena…Determination the
Qualitative rotation of glucose and fructose.
6
: Lipids. Qualitative tests for Lipids
7
8
10
11
1-The solubility of lipids
2- Acrolein formation (Acrolein test):
3) Denstan test:
3-Tests for unsaturated fatty acids. 1-Copper acetate test:
Quantitative Analysis of Lipids1The determination of -Saponification number of a fat
1- The determination of Iodine number of a fat
Rancidity of Lipids(Determine the rancidity in the fat
1. Determination of the Peroxide number: of a fat 2. Determination of Acid number of a fat
3-Cries test for detection of rancid lipid
Proteins & Amino acids
Qualitative tests of Proteins & Amino acids
1- Ninhydrintest
2--The Biuret test for peptide bonds
3-Xanthoproteic reaction
4-Glyoxylic acid test
Qualitative tests of Proteins & Amino acids
5. Pauly's test:
6. Sakaguchi test:
7. Lead acetate test:
8. Nitro prusside test:
Precipitation of Proteins
1. Precipitation by heavy metals:
2. Precipitation by acidic reagents:
3. Precipitation by concentrated metallic acid:
4. Precipitation by Ethanol (alcohol):
5. Precipitation by metallic salts:
a. Half saturation: B.Full saturation test:
12
6- Denaturation of of portions
Clinical Biochemistry Assay
Blood collection
Instruments used to measure light intensity (spectrophotometer)
13
14
1-Estimation of blood cholesterol by Lieberman bur chard method:
15
2. -Estimation of blood glucose by King-Garnner method
16
Electrophoresis principle
3-Estimation of blood protein by Biuret method
Estimation of blood albumin
4-Estimation of blood Urea by Nessler method
17
18
5-Estimation of blood Amylase activity
19
6-Estimation of blood Calcium
7-Estimation of blood Phosphorus
20
21
8-Estimation of blood Bilirubin (total, direct & indirect)
22
9--Estimation of blood uric acid
23
10- Estimation of Blood Transaminase (GOT & GPT.)
24
11- Estimation of Serum ACP
25
12- Estimation of Serum ALP
26
27
-Estimation
of
Vitamin
C
2, 6-dichlorophenol endo phenol dye.
Estimation of Blood creatinine
28
Estimation of Blood TG
in
urine
by
using
29
Estimation of Blood LDH
30
Estimation of Blood CK
31
Estimation of Blood lipase
Estimation of blood electrolyte (Na+, K+, & Cl-)
Estimation of Blood glucose by Hb1C
Estimation of Blood sex hormones
(FSH, estrogen, progestron, & LH)
Estimation of Blood sex hormones
(thyroxin, T3, T4, & free T3, & T4 )
Recommended Reading
1- David L. Nelson and Michael M. Cox, (, 2009). 5th edition. Lehninger Principles of
Biochemistry. Macmillan Worth Publishers
1-Voet, Voet and Pratt,( 2008). Fundamentals of Biochemistry, 3rd Edition, Wiley,.
2-MCKEE & MCKEE = MCKEE, TRUDY, & JAMES R. MCKEE. ( 2011) . 5th ed..
Biochemistry: The Molecular Basis of Life. New York: Oxford University Press.
3-FERGUSON = FERGUSON, JOHN B. Laboratory ( 2012).Manual — Biology 301:
Biochemistry. Annandale-on-Hudson NY: Bard College,
4-NINFA ET AL. = NINFA, ALEXANDER J., DAVID P. BALLOU, & MARILEE BENORE. (2010).
2nd ed. Fundamental Laboratory Approaches for Biochemistry and Biotechnology..
Hoboken NJ: John Wiley & Sons,
5-. Practical Clinical Biochemistry - Harold Varley, CBS, New Delhi.
6. David L. Nelson and Michael M. Cox, (, 2005). 5th edition. Lehninger Principles of
Biochemistry. Macmillan Worth Publishers L
7 Rober K. Murray, Daryl K. Grammer(2008). Harper’s Biochemistry-,
edition. McGraw Hill, Lange Medical Books..
25th